Exact enumeration of three-dimensional lattice proteins

DOI10.1016/J.CPC.2004.09.011MaRDI QIDQ709694zbMATHOpenAlexDBLPWikidataFDO

Authors Reinhard Schiemann, Michael Bachmann, Wolfhard Janke

Publication date 18 October 2010

Published in Computer Physics Communications (Search for Journal in Brave)

Full work available at URL https://arxiv.org/abs/cond-mat/0501401

zbMATH Keywords

polymersself-avoiding walksHP modelcontact mapslattice proteins

Mathematics Subject Classification ID

Biochemistry, molecular biology (92C40) Statistical mechanics of polymers (82D60) Molecular structure (graph-theoretic methods, methods of differential topology, etc.) (92E10)

Abstract: We present an algorithm for the exhaustive enumeration of all monomer sequences and conformations of short lattice proteins as described by the hydrophobic-polar (HP) model. The algorithm is used for an exact identification of all designing sequences of HP proteins consisting of up to 19 monomers whose conformations are represented by interacting self-avoiding walks on the simple cubic lattice. Employing a parallelized implementation on a Linux cluster, we generate the complete set of contact maps of such walks.

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Cites work

• scientific article; zbMATH DE number 960151 (Why is no real title available?)
• Self-avoiding walks on the simple cubic lattice
• Universal amplitude ratios for three-dimensional self-avoiding walks

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(6)

• A deterministic algorithm for constrained enumeration of transmembrane protein folds
• scientific article; zbMATH DE number 2130523 (Why is no real title available?)
• Efficient algorithm for computing exact partition functions of lattice polymer models
• Exact enumeration of Hamiltonian walks on the \(4\times 4\times 4\) cube and applications to protein folding
• Three-dimensional off-lattice AB model protein with the 89-residue Fibonacci sequence
• Parallel algorithm for calculation of the exact partition function of a lattice polymer

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